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Jin H, Tian Y, Zhang Y, Zhang R, Zhao H, Yang X, Song X, Dimitrov Y, Wu YE, Gao Q, Liu J, Zhang J, He Z. Genome-Wide Association Mapping of Processing Quality Traits in Common Wheat ( Triticum aestivum L.). Genes (Basel) 2023; 14:1816. [PMID: 37761956 PMCID: PMC10530800 DOI: 10.3390/genes14091816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2-42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection.
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Affiliation(s)
- Hui Jin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yuanyuan Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Yan Zhang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Haibin Zhao
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Xue Yang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Xizhang Song
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yordan Dimitrov
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yu-e Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Qiang Gao
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Jumei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
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Bouchet AS, Laperche A, Bissuel-Belaygue C, Baron C, Morice J, Rousseau-Gueutin M, Dheu JE, George P, Pinochet X, Foubert T, Maes O, Dugué D, Guinot F, Nesi N. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed. BMC Genet 2016; 17:131. [PMID: 27628849 PMCID: PMC5024496 DOI: 10.1186/s12863-016-0432-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Background Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Results Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Conclusions Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition levels on seed yield-related traits under our experimental conditions. Nevertheless, critical genomic regions associated with yield that were stable across environments were identified in rapeseed. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anne Laperche
- AGROCAMPUS OUEST, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France.
| | | | - Cécile Baron
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | - Jérôme Morice
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | | | - Jean-Eric Dheu
- Limagrain Europe, Ferme de l'Etang, 77390, Verneuil-l'Etang, France
| | - Pierre George
- Biogemma, Chemin de Panedautes, 31700, Mondonville, France
| | - Xavier Pinochet
- Terres Inovia, Avenue Lucien Brétignières, 78850, Thiverval Grignon, France
| | - Thomas Foubert
- Euralis, Chemin de Panedautes, 31700, Mondonville, France
| | - Olivier Maes
- Maisadour Semences, Route de Saint Sever, BP27, 40001, Mont de Marsan Cedex, France
| | - Damien Dugué
- RAGT R2n, Rue Emile Singla, BP 3331, 12033, Rodez, France
| | - Florent Guinot
- Syngenta, Chemin de l'Hobit, 31790, Saint-Sauveur, France
| | - Nathalie Nesi
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
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Jin H, Wen W, Liu J, Zhai S, Zhang Y, Yan J, Liu Z, Xia X, He Z. Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population. FRONTIERS IN PLANT SCIENCE 2016; 7:1032. [PMID: 27486464 PMCID: PMC4949415 DOI: 10.3389/fpls.2016.01032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.
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Affiliation(s)
- Hui Jin
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural UniversityBeijing, China
| | - Weie Wen
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shengnan Zhai
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yan Zhang
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jun Yan
- Wheat and Maize Research Center, Institute of Cotton Research, Chinese Academy of Agricultural SciencesAnyang, China
| | - Zhiyong Liu
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural UniversityBeijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China officeBeijing, China
- *Correspondence: Zhonghu He
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